miga-base 0.7.26.2 → 1.0.3.0

data/utils/multitrim/multitrim.yml

@@ -0,0 +1,13 @@
+name: multitrim
+dependencies:
+  - faqcs
+  - falco
+  - seqtk
+  - fastp
+  - pigz
+  - multitrim
+  
+channels:
+  - conda-forge
+  - bioconda
+  - kgerhardt

data/utils/requirements.txt

@@ -13,9 +13,10 @@ Prodigal	prodigal	http://prodigal.ornl.gov
 MCL		mcl		http://micans.org/mcl/
 Barrnap		barrnap		http://www.vicbioinformatics.com/software.barrnap.shtml
 IDBA (reads)	idba_ud		http://i.cs.hku.hk/~alse/hkubrg/projects/idba
-Scythe (reads)	scythe		https://github.com/vsbuffalo/scythe				Required version: 0.991+
-FastQC (reads)	fastqc		http://www.bioinformatics.babraham.ac.uk/projects/fastqc
-SolexaQA++ (reads)	SolexaQA++	http://solexaqa.sourceforge.net				Required version: v3.1.3+
+FaQCs (reads)	FaQCs		https://github.com/LANL-Bioinformatics/FaQCs
+Falco (reads)	falco		https://github.com/smithlabcode/falco
+Seqtk (reads)	seqtk		https://github.com/lh3/seqtk
+Fastp (reads)	fastp		https://github.com/OpenGene/fastp
 OpenJDK (rdp)	java		https://adoptopenjdk.net/					Any Java VM would work
 MyTaxa (mytaxa)	MyTaxa		http://enve-omics.ce.gatech.edu/mytaxa
 Krona (mytaxa)	ktImportText	https://github.com/marbl/Krona/wiki

data/utils/subclade/pipeline.rb

@@ -17,10 +17,10 @@ module MiGA::SubcladeRunner::Pipeline
       metric_res = project.result(par[0]) or raise "Incomplete step #{par[0]}"
       Zlib::GzipReader.open(metric_res.file_path(:matrix)) do |ifh|
         ifh.each_line do |ln|
-          next if ln =~ /^metric\t/
+          next if ln =~ /^a\tb\tvalue\t/
 
           r = ln.chomp.split("\t")
-          ofh.puts "G>#{r[1]}\tG>#{r[2]}\t#{r[3]}" if r[3].to_f >= par[1]
+          ofh.puts "G>#{r[0]}\tG>#{r[1]}\t#{r[2]}" if r[2].to_f >= par[1]
         end
       end
       ofh.close

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.26.2
+  version: 1.0.3.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-01 00:00:00.000000000 Z
+date: 2021-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -110,8 +110,12 @@ files:
 - lib/miga.rb
 - lib/miga/_data/aai-intax-blast.tsv.gz
 - lib/miga/_data/aai-intax-diamond.tsv.gz
+- lib/miga/_data/aai-intax.blast.tsv.gz
+- lib/miga/_data/aai-intax.diamond.tsv.gz
 - lib/miga/_data/aai-novel-blast.tsv.gz
 - lib/miga/_data/aai-novel-diamond.tsv.gz
+- lib/miga/_data/aai-novel.blast.tsv.gz
+- lib/miga/_data/aai-novel.diamond.tsv.gz
 - lib/miga/cli.rb
 - lib/miga/cli/action.rb
 - lib/miga/cli/action/about.rb
@@ -137,6 +141,7 @@ files:
 - lib/miga/cli/action/doctor.rb
 - lib/miga/cli/action/doctor/base.rb
 - lib/miga/cli/action/edit.rb
+- lib/miga/cli/action/env.rb
 - lib/miga/cli/action/files.rb
 - lib/miga/cli/action/find.rb
 - lib/miga/cli/action/generic.rb
@@ -187,6 +192,7 @@ files:
 - lib/miga/json.rb
 - lib/miga/lair.rb
 - lib/miga/metadata.rb
+- lib/miga/parallel.rb
 - lib/miga/project.rb
 - lib/miga/project/base.rb
 - lib/miga/project/dataset.rb
@@ -240,6 +246,7 @@ files:
 - test/lair_test.rb
 - test/metadata_test.rb
 - test/net_test.rb
+- test/parallel_test.rb
 - test/project_test.rb
 - test/remote_dataset_test.rb
 - test/result_stats_test.rb
@@ -374,9 +381,11 @@ files:
 - utils/enveomics/Scripts/FastA.split.rb
 - utils/enveomics/Scripts/FastA.subsample.pl
 - utils/enveomics/Scripts/FastA.tag.rb
+- utils/enveomics/Scripts/FastA.toFastQ.rb
 - utils/enveomics/Scripts/FastA.wrap.rb
 - utils/enveomics/Scripts/FastQ.filter.pl
 - utils/enveomics/Scripts/FastQ.interpose.pl
+- utils/enveomics/Scripts/FastQ.maskQual.rb
 - utils/enveomics/Scripts/FastQ.offset.pl
 - utils/enveomics/Scripts/FastQ.split.pl
 - utils/enveomics/Scripts/FastQ.tag.rb
@@ -405,6 +414,7 @@ files:
 - utils/enveomics/Scripts/Table.df2dist.R
 - utils/enveomics/Scripts/Table.filter.pl
 - utils/enveomics/Scripts/Table.merge.pl
+- utils/enveomics/Scripts/Table.prefScore.R
 - utils/enveomics/Scripts/Table.replace.rb
 - utils/enveomics/Scripts/Table.round.rb
 - utils/enveomics/Scripts/Table.split.pl
@@ -413,18 +423,28 @@ files:
 - utils/enveomics/Scripts/VCF.SNPs.rb
 - utils/enveomics/Scripts/aai.rb
 - utils/enveomics/Scripts/ani.rb
+- utils/enveomics/Scripts/anir.rb
 - utils/enveomics/Scripts/clust.rand.rb
 - utils/enveomics/Scripts/gi2tax.rb
 - utils/enveomics/Scripts/in_silico_GA_GI.pl
 - utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz
 - utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz
 - utils/enveomics/Scripts/lib/enveomics.R
+- utils/enveomics/Scripts/lib/enveomics_rb/anir.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb
 - utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/errors.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb
 - utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/match.rb
 - utils/enveomics/Scripts/lib/enveomics_rb/og.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb
 - utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb
 - utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb
-- utils/enveomics/Scripts/lib/enveomics_rb/stat.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/stats.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb
+- utils/enveomics/Scripts/lib/enveomics_rb/utils.rb
 - utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb
 - utils/enveomics/Scripts/ogs.annotate.rb
 - utils/enveomics/Scripts/ogs.core-pan.rb
@@ -432,7 +452,9 @@ files:
 - utils/enveomics/Scripts/ogs.mcl.rb
 - utils/enveomics/Scripts/ogs.rb
 - utils/enveomics/Scripts/ogs.stats.rb
+- utils/enveomics/Scripts/rbm-legacy.rb
 - utils/enveomics/Scripts/rbm.rb
+- utils/enveomics/Scripts/sam.filter.rb
 - utils/enveomics/Tests/Makefile
 - utils/enveomics/Tests/Mgen_M2288.faa
 - utils/enveomics/Tests/Mgen_M2288.fna
@@ -470,6 +492,7 @@ files:
 - utils/enveomics/enveomics.R/R/cliopts.R
 - utils/enveomics/enveomics.R/R/df2dist.R
 - utils/enveomics/enveomics.R/R/growthcurve.R
+- utils/enveomics/enveomics.R/R/prefscore.R
 - utils/enveomics/enveomics.R/R/recplot.R
 - utils/enveomics/enveomics.R/R/recplot2.R
 - utils/enveomics/enveomics.R/R/tribs.R
@@ -495,6 +518,7 @@ files:
 - utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd
 - utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd
 - utils/enveomics/enveomics.R/man/enve.growthcurve.Rd
+- utils/enveomics/enveomics.R/man/enve.prefscore.Rd
 - utils/enveomics/enveomics.R/man/enve.prune.dist.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd
@@ -520,6 +544,7 @@ files:
 - utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd
 - utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd
+- utils/enveomics/enveomics.R/man/enve.selvector.Rd
 - utils/enveomics/enveomics.R/man/enve.tribs.Rd
 - utils/enveomics/enveomics.R/man/enve.tribs.test.Rd
 - utils/enveomics/enveomics.R/man/enve.truncate.Rd
@@ -536,6 +561,10 @@ files:
 - utils/enveomics/manifest.json
 - utils/find-medoid.R
 - utils/index_metadata.rb
+- utils/multitrim/Multitrim How-To.pdf
+- utils/multitrim/README.md
+- utils/multitrim/multitrim.py
+- utils/multitrim/multitrim.yml
 - utils/mytaxa_scan.R
 - utils/mytaxa_scan.rb
 - utils/plot-taxdist.R
@@ -575,7 +604,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.4
+rubygems_version: 3.1.6
 signing_key: 
 specification_version: 4
 summary: MiGA

data/utils/enveomics/Scripts/lib/enveomics_rb/stat.rb

@@ -1,30 +0,0 @@
-
-module Enve
-  class Stat
-    # Generates a random number from the +dist+ distribution with +params+
-    # parameters. This is simply a wrapper to the r_* functions below.
-    def self.rand(dist=:unif, *params)
-      send("r_#{dist}", *params)
-    end
-
-    # Generates a random number from the uniform distribution between +min+ and
-    # +max+. By default generates random numbers between 0.0 and 1.0.
-    def self.r_unif(min=0.0, max=1.0)
-      min + (max-min)*Random::rand
-    end
-    
-    # Generates a random number from the geometric distribution with support
-    # {0, 1, 2, ...} and probability of success +p+.
-    def self.r_geom(p)
-      (Math::log(1.0 - rand)/Math::log(1.0-p) - 1.0).ceil
-    end
-
-    # Generates a random number from the shifted geometric distribution with
-    # support {1, 2, 3, ...} and probability of success +p+.
-    def self.r_sgeom(p)
-      (Math::log(1.0 - rand)/Math::log(1.0-p)).ceil
-    end
-    
-  end
-end
-